Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1756 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0400215181 sf0400214181 4 215181 3.45E-07 3.45E-07
vg1126876944 sf1126405331 11 26876944 4.04E-07 4.04E-07
vg0200811680 sf0200811680 2 811680 2.33E-06 2.33E-06
vg1121624353 sf1121158230 11 21624353 2.42E-06 2.42E-06
vg0141225239 sf0141224196 1 41225239 3.66E-06 3.66E-06
vg0504650681 sf0504650658 5 4650681 3.78E-06 3.78E-06
vg0222060582 sf0222054713 2 22060582 4.98E-06 4.98E-06